Refusing to hire him would be overzealous in any Catholic school. But it’s especially jarring at Fontbonne. For decades, this school has been a beacon of acceptance, a place where young women are empowered and taught to question everything, alumnae say. There, the Sign of the Cross is a gender-neutral affair. Instead of naming Father and Son, it goes, “In the name of the Creator, The Redeemer, and the Holy Spirit.”

Though she is Jewish, Nikki Tishler felt embraced at Fontbonne. “The Theology Department is where I found my home,” said Tishler, who graduated in 2007. “The social justice mission of the school spoke to me, it fostered me to become an activist.’’

Some teachers were gay, though they didn’t make it official like Barrett did, naming his husband as emergency contact. None of the former students I spoke to recall much of a focus on social issues. When Massachusetts legalized gay marriage in 2003, Tishler recalled it as “a moment of celebration,” for gay and straight students, and for teachers, too.

Run by the Sisters of St. Joseph, Fontbonne has long fostered the values the new pope has been voicing with such captivating eloquence. Which is why Barrett’s complaint has been such a seismic event for Fontbonne and its alumnae. They are angry about his treatment. And they are angry that the school is being cast as an intolerant place. Many of them believe Catholic higher-ups must have directed school leaders to rescind the job offer.

The school did seek guidance from the diocese before acting, said Greg Chambers, assistant head of the school. Though the diocese has no official sway over the school, it’s easy to imagine the nuns who oversee Fontbonne — the kind of nuns who have been the target of chilling papal scrutiny in recent years — not wanting to take the risk here.

In any case, Chambers toed the official line Friday afternoon. “We are a school guided by the beliefs of the Catholic Church, and marriage between persons of the same sex is contrary to the teachings of the church,” he said.

It’s hard to reconcile some of those beliefs with a social justice mission as strong as Fontbonne’s. Many who love the school don’t try, choosing the latter over the former without hesitation.

They’re like many Catholics in this country, embracing the church’s messages of love and justice, but parting ways with it on social issues. The pews are full of them: gays and lesbians; people who use birth control; abortion rights supporters; people who are divorced; those who long for the ordination of women.

Their ranks will grow in coming decades. Fissures like the one opened at Fontbonne Academy will be more frequent, and more damaging. If the church is to thrive, it will have to embrace, or at least adapt to, the change those parishioners represent.

I held out little hope of that when Benedict was pope. I’m convinced Francis is leading his flock toward a place where the Matthew Barretts of the world will find not just love — and jobs — but full lives in the church.

And when it gets there, the loudest cheers will rise from women who found their life’s mission at a prep school in Milton.